scholarly journals Dynamic DNA Origami Devices

2018 ◽  
Author(s):  
Heini Ijäs ◽  
Sami Nummelin ◽  
Boxuan Shen ◽  
Mauri A. Kostiainen ◽  
Veikko Linko
Keyword(s):  
Rapid Evolution ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Dna Assembly ◽  
Plasmonic Sensors ◽  
Nanophotonic Devices ◽  
Dna Strands ◽  
Materials Research ◽  
External Stimuli ◽  
Structural Dna Nanotechnology

Structural DNA nanotechnology provides an excellent foundation for diverse nanoscale shapes that can be used in various bioapplications and materials research. From all existing DNA assembly techniques, DNA origami has proven to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA has drastically advanced, and therefore, more and more complex DNA-based systems have become accessible. So far, vast majority of the demonstrated DNA origami frameworks are static by nature, but interestingly, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that perform controlled translational or rotational movement triggered by predefined DNA strands, various molecular interactions and/or other external stimuli such as light, pH, temperature and electromagnetic fields. The rapid evolution of such dynamic DNA origami tools will undoubtedly have a significant impact on molecular scale precision measurements, targeted drug delivery and diagnostics, but they can also play a role in development of optical/plasmonic sensors, nanophotonic devices and nanorobotics for numerous different tasks.

scholarly journals Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems

2018 ◽  
Vol 19 (7) ◽  
pp. 2114 ◽  
Author(s):  
Heini Ijäs ◽  
Sami Nummelin ◽  
Boxuan Shen ◽  
Mauri Kostiainen ◽  
Veikko Linko
Keyword(s):  
Dna Sequences ◽  
Rapid Evolution ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Dna Assembly ◽  
Stimuli Responsive ◽  
Nanoscale Structures ◽  
Displacement Reactions ◽  
Materials Research ◽  
External Stimuli

DNA nanotechnology provides an excellent foundation for diverse nanoscale structures that can be used in various bioapplications and materials research. Among all existing DNA assembly techniques, DNA origami proves to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA advanced drastically, and therefore, more and more complex DNA-based systems became accessible. So far, the vast majority of the demonstrated DNA origami frameworks are static by nature; however, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that exhibit controlled translational or rotational movement when triggered by predefined DNA sequences, various molecular interactions, and/or external stimuli such as light, pH, temperature, and electromagnetic fields. The rapid evolution of such dynamic DNA origami tools will undoubtedly have a significant impact on molecular-scale precision measurements, targeted drug delivery and diagnostics; however, they can also play a role in the development of optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.

scholarly journals DNA Origami Nanomachines

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1766 ◽  
Author(s):  
Masayuki Endo ◽  
Hiroshi Sugiyama
Keyword(s):  
Dna Sequences ◽  
Molecular Motors ◽  
Molecular Machines ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Molecular Systems ◽  
Nanoscale Structures ◽  
Research Fields ◽  
Dna Strands ◽  
External Stimuli

DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to perform linear, rotational, and reciprocating movements. Furthermore, complicated molecular systems have been created on DNA nanostructures by arranging multiple molecules and molecular machines precisely to mimic biological systems. Currently, DNA nanomachines, such as molecular motors, are operated on DNA nanostructures. Dynamic DNA nanostructures that have a mechanically controllable system have also been developed. In this review, we describe recent research on new DNA nanomachines and nanosystems that were built on designed DNA nanostructures.

scholarly journals Programming Structured DNA Assemblies to Probe Biophysical Processes

2019 ◽  
Vol 48 (1) ◽  
pp. 395-419 ◽  
Author(s):  
Eike-Christian Wamhoff ◽  
James L. Banal ◽  
William P. Bricker ◽  
Tyson R. Shepherd ◽  
Molly F. Parsons ◽  
...  
Keyword(s):  
Structural Biology ◽  
Energy Transport ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Design And Synthesis ◽  
Copy Numbers ◽  
Target Nucleic Acid ◽  
Biophysical Processes ◽  
Fully Automatic ◽  
Structural Dna Nanotechnology

Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1–100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.

scholarly journals The Effects of Overhang Placement and Multivalency on Cell Labeling by DNA Origami

Nanoscale ◽  
2021 ◽  
Author(s):  
Ying Liu ◽  
Piyumi Wijesekara-Kankanange ◽  
Sriram Kumar ◽  
Weitao Wang ◽  
Xi Ren ◽  
...  
Keyword(s):  
Growth Factors ◽  
Cell Membrane ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Cell Labeling ◽  
Structural Dna Nanotechnology

Through targeted binding to the cell membrane, structural DNA nanotechnology has the potential to guide and affix biomolecules such as drugs, growth factors and nanobiosensors to the surfaces of cells....

scholarly journals DNA nanochannels

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 503 ◽  
Author(s):  
Dianming Wang ◽  
Yiyang Zhang ◽  
Dongsheng Liu
Keyword(s):  
Dna Nanotechnology ◽  
Transmembrane Proteins ◽  
Current Situation ◽  
Dna Origami ◽  
Promising Method ◽  
Fundamental Interest ◽  
Development History ◽  
Different Types ◽  
Structural Dna Nanotechnology ◽  
Biological Channels

Transmembrane proteins are mostly nanochannels playing a highly important role in metabolism. Understanding their structures and functions is vital for revealing life processes. It is of fundamental interest to develop chemical devices to mimic biological channels. Structural DNA nanotechnology has been proven to be a promising method for the preparation of fine DNA nanochannels as a result of the excellent properties of DNA molecules. This review presents the development history and current situation of three different types of DNA nanochannel: tile-based nanotube, DNA origami nanochannel, and DNA bundle nanochannel.

scholarly journals Revealing thermodynamics of DNA origami folding via affine transformations

2020 ◽  
Vol 48 (10) ◽  
pp. 5268-5280 ◽  
Author(s):  
Jacob M Majikes ◽  
Paul N Patrone ◽  
Daniel Schiffels ◽  
Michael Zwolak ◽  
Anthony J Kearsley ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Structural Defects ◽  
Affine Transformations ◽  
Fluorescent Reporter ◽  
Self Assembling ◽  
Heat Capacity Changes ◽  
Quantitative Understanding ◽  
Structural Dna Nanotechnology

Abstract Structural DNA nanotechnology, as exemplified by DNA origami, has enabled the design and construction of molecularly-precise objects for a myriad of applications. However, limitations in imaging, and other characterization approaches, make a quantitative understanding of the folding process challenging. Such an understanding is necessary to determine the origins of structural defects, which constrain the practical use of these nanostructures. Here, we combine careful fluorescent reporter design with a novel affine transformation technique that, together, permit the rigorous measurement of folding thermodynamics. This method removes sources of systematic uncertainty and resolves problems with typical background-correction schemes. This in turn allows us to examine entropic corrections associated with folding and potential secondary and tertiary structure of the scaffold. Our approach also highlights the importance of heat-capacity changes during DNA melting. In addition to yielding insight into DNA origami folding, it is well-suited to probing fundamental processes in related self-assembling systems.

Structural DNA nanotechnology: Immobile Holliday junctions to artificial robots

2022 ◽  
Vol 22 ◽  
Author(s):  
Raghu Pradeep Narayanan ◽  
Leeza Abraham
Keyword(s):  
Dna Nanotechnology ◽  
Building Blocks ◽  
Holliday Junctions ◽  
Dna Origami ◽  
Building Structures ◽  
Dna Nanostructures ◽  
3 Dimensional ◽  
Scientific World ◽  
2D And 3D ◽  
Structural Dna Nanotechnology

Abstreact: DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds off from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the ‘tile’ based approach covering 1D, 2D, and 3D building blocks, after which, the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through the various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.

Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research

2018 ◽  
Vol 20 (1) ◽  
pp. 375-401 ◽  
Author(s):  
Yonggang Ke ◽  
Carlos Castro ◽  
Jong Hyun Choi
Keyword(s):  
Biomedical Research ◽  
Self Assembly ◽  
Biomedical Applications ◽  
Dna Nanotechnology ◽  
Dna Nanostructures ◽  
Considerable Effort ◽  
Artificial Nanostructures ◽  
Active Pursuit ◽  
External Stimuli ◽  
Structural Dna Nanotechnology

Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson–Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli. Researchers have devoted considerable effort to exploring the usability of DNA nanostructures in biomedical research. We review the basic design methods for fabricating both static and dynamic DNA nanostructures, along with their biomedical applications in fields such as biosensing, bioimaging, and drug delivery.

scholarly journals Generating DNA Origami Nanostructures through Shape Annealing

2021 ◽  
Vol 11 (7) ◽  
pp. 2950
Author(s):  
Bolutito Babatunde ◽  
D. Sebastian Arias ◽  
Jonathan Cagan ◽  
Rebecca E. Taylor
Keyword(s):  
Self Assembly ◽  
Design Space ◽  
Simulated Annealing Algorithm ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Design Tools ◽  
Dna Nanostructures ◽  
Formal Approach ◽  
Annealing Algorithm ◽  
Structural Dna Nanotechnology

Structural DNA nanotechnology involves the design and self-assembly of DNA-based nanostructures. As a field, it has progressed at an exponential rate over recent years. The demand for unique DNA origami nanostructures has driven the development of design tools, but current CAD tools for structural DNA nanotechnology are limited by requiring users to fully conceptualize a design for implementation. This article introduces a novel formal approach for routing the single-stranded scaffold DNA that defines the shape of DNA origami nanostructures. This approach for automated scaffold routing broadens the design space and generates complex multilayer DNA origami designs in an optimally driven way, based on a set of constraints and desired features. This technique computes unique designs of DNA origami assemblies by utilizing shape annealing, which is an integration of shape grammars and the simulated annealing algorithm. The results presented in this article illustrate the potential of the technique to code desired features into DNA nanostructures.

scholarly journals Strategies to Build Hybrid Protein–DNA Nanostructures

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1332
Author(s):  
Armando Hernandez-Garcia
Keyword(s):  
Dynamic Systems ◽  
Dna Nanotechnology ◽  
Chemical Properties ◽  
Hybrid Nanostructures ◽  
Advanced Materials ◽  
Dna Nanostructures ◽  
Hybrid Protein ◽  
Structural Protein ◽  
The Individual ◽  
Structural Dna Nanotechnology

Proteins and DNA exhibit key physical chemical properties that make them advantageous for building nanostructures with outstanding features. Both DNA and protein nanotechnology have growth notably and proved to be fertile disciplines. The combination of both types of nanotechnologies is helpful to overcome the individual weaknesses and limitations of each one, paving the way for the continuing diversification of structural nanotechnologies. Recent studies have implemented a synergistic combination of both biomolecules to assemble unique and sophisticate protein–DNA nanostructures. These hybrid nanostructures are highly programmable and display remarkable features that create new opportunities to build on the nanoscale. This review focuses on the strategies deployed to create hybrid protein–DNA nanostructures. Here, we discuss strategies such as polymerization, spatial directing and organizing, coating, and rigidizing or folding DNA into particular shapes or moving parts. The enrichment of structural DNA nanotechnology by incorporating protein nanotechnology has been clearly demonstrated and still shows a large potential to create useful and advanced materials with cell-like properties or dynamic systems. It can be expected that structural protein–DNA nanotechnology will open new avenues in the fabrication of nanoassemblies with unique functional applications and enrich the toolbox of bionanotechnology.

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